There are both good and bad to "all guns shoot same ammo".
If you and your wife are on the run, and you've got a 45 and she's got a 9, there's not a large amount of difference between carrying 100 rounds of each, or carrying 200 rounds of one. But, if you get down to having only 14 round of 9 left, since you have a 45, she's the only one with a loaded gun. If you both had 9s, then you both could have some ammo, even if neither gun was full-loaded.
It's the same with rifle/pistol. If all I have left is 10 rounds of 357, I can put them in my carbine, if I think I might need to shoot something a hundred yards away, or put them in my pistol, if I need to stick my gun in my waistband and pull my shirt over it. I don't have that option, if my rifle and my pistol shoot different calibers.
There are disadvantages, though. A 357 out of a 20" lever gun's barrel is better than out of a 6" revolver, but it is nowhere near as good as a 30/06 out of a 22" bolt gun. Unless you have some strange pistol (Contender, in 223, or BRF in 45/70, for example) chambered in rifle rounds, by definition your long gun is going to be a pistol cartridge. Pistol cartridges just aren't that powerful. With the most powerful options (357 or 44 magnum, or 454) you are going to be lucky if you can hit something more than 150 yards away. While a "real" rifle cartridge (270, 30/06, etc) will reach out to 500 or more.
So, there are plus and minuses to both ways of doing it. You must decide for yourself which is better for you.